GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Klebsiella michiganensis M5al

Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__Koxy:BWI76_RS03270
          Length = 376

 Score =  315 bits (808), Expect = 1e-90
 Identities = 188/381 (49%), Positives = 241/381 (63%), Gaps = 32/381 (8%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           MATV+  K  + Y    K AV  +D+ I DGEF+V VGPSGC KST+LRM+AGLED++GG
Sbjct: 1   MATVSLRKIEKRYENGFK-AVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGG 59

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            I IG+R V  LPPKDR IAMVFQNYALYPH TV DNM F LK+   PK EI+++VE+AA
Sbjct: 60  EIYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAA 119

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           + L++T+ L RKPK +SGGQRQRVA+GRAIVR+P VFL DEPLSNLDAKLRVS R +IA 
Sbjct: 120 EKLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQ 179

Query: 181 LQRRL-----GITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGF 235
           L R L       T +YVTHDQ EA+T+GDR+ VL  G + QVD+P ++Y+ P N FVA F
Sbjct: 180 LHRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASF 239

Query: 236 IGSPAMNLVEVPITDGGVKFGNSVVPVNREALSAADKG-------DRTVTVGVRPEHFDV 288
           IGSP++NL++  I     +    + P   E L    K        ++ V  G+RPEH   
Sbjct: 240 IGSPSINLIDTAIRKNNERLYVEIAP-GVEILIPHSKQVLLEGYINKPVCFGIRPEHI-- 296

Query: 289 VELGGAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQV 348
                    SL+ D  D      V + VVE +G++ ++Y    VGG  K+L+ RV+ + +
Sbjct: 297 ---------SLASDDDDLNTFEGV-LTVVENMGSEKFLYFI--VGG--KELIARVDTQDI 342

Query: 349 P--EKGSTLHVVPRPGETHVF 367
                G TL         HVF
Sbjct: 343 NPFHIGKTLRFNLNTAFCHVF 363


Lambda     K      H
   0.317    0.135    0.379 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 377
Number of extensions: 16
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 377
Length of database: 376
Length adjustment: 30
Effective length of query: 347
Effective length of database: 346
Effective search space:   120062
Effective search space used:   120062
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory